[gmx-users] Numbering in xtc and in conf.gro. Does it coincide?

David van der Spoel spoel at xray.bmc.uu.se
Tue Jan 20 15:54:23 CET 2009

Vitaly Chaban wrote:
>> Source code file: matio.c, line: 533
>> Fatal error:
>> Lo: 0.000000, Mid: 1.000000, Hi: 1.000000
>> Although nclust.xvg, maxclust.xvg, avclust.xvg are created and seem
>> adequate.
>> However what could the above error indicate?
>> that all atoms belong to the same cluster.
> Yes, it's true in my case.
> And one more question about index file. If xtc-qrps is used and only
> the groups of interest are output in xtc file, should the atoms in the
> index file be renumbered or not?
> For example, if in conf.gro we have atoms of interest with numbers 4,5,6
> and didn't write atoms 1,2,3 to the xtc file, should we then refer to the
> wanted atoms as 4,5,6 (as it was initially) or 1,2,3 (due to the
> shift...)?
> In other words, is information about the initial (in conf.gro)
> numbering of molecules present in the xtc trajectory file? Looking at
> the xtc using gmxdump I see the numbering always start with zero in
> spite of the xtc-qrps arguments.
All files number from 0 to natom-1. You have to do the remapping.
> Thank you.
> Vitaly
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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